RepeatFinder

A python package to quickly find repeats in a DNA sequence

Installing

To get, you can either install via pip with the command:

pip install repeatfinder

or you can fetch the source, compile, theninstall the module:

git clone https://github.com/deprekate/RepeatFinder
cd RepeatFinder
python3 setup.py install

Usage

Import and use the module as normal

import repeatfinder as rf
my_reps = rf.get_repeats('GGGGGGGGGGGGcAAAAAAAAAAAAgctacgatggagctgacGGGGGGGGGGGGtAAAAAAAAAAAAt')

You can even allow for gaps in the repeats by using the keyword gap

my_reps = rf.get_repeats('GGGGGGGGGGGGcAAAAAAAAAAAAgctacgatggagctgacGGGGGGGGGGGGtAAAAAAAAAAAAt', gap = 1)

The return values are an iterable list containing four-tuples, where the first and second tuple correspond to the coordinates of one of the repeat pairs, and the third and fourth correspond to the other repeat. The list is sorted with the higher scoring repeat pairs coming first.

To run the example script:

python3 test.py

and the output would be the following

non gapped repeats
(1, 12, 43, 54)
(1, 11, 44, 54)
(2, 12, 43, 53)
(14, 25, 56, 67)
(14, 24, 57, 67)
(15, 25, 56, 66)
gapped repeats
(1, 25, 43, 67)
(1, 11, 44, 54)
(2, 12, 43, 53)
(14, 24, 57, 67)
(15, 25, 56, 66)